How to generate this graphic - number of viral reads mapped to genome

Question

[ermela.paparisto]

Hello,

I have been trying to figure out how to make a plot like this for days! It bsically shows rna seq data mapped to the sars-cov-2 genome and shows the coverage (number of viral reads) for each genome position using a line graph. A map of the genome and the protein coding regions are shown at the bottom. Source is https://www.sciencedirect.com/science/article/pii/S009286742030489X and its figure 1b Can anyone shed any light on how to create this plot? I am guessing its done in R. Any advise or tutorial suggestions are greatly appreciated!

[lieven.sterck]

I assume they plotted the output of some coverage calculation in a graph.

Perhaps have a look in this post: How to plot coverage and depth statistics of a bam file , there might some useful approaches mentioned in it